Taken from “Phineas and Candace’s Father” from 1234 Friendship Creation Blog, slightly modified.
Not Lawrence Fletcher, their step-father. Their biological father, the one who caused Linda Flynn to get pregnant with those two. According to a lot of sources, there are two possibilities, that he either died or was still alive but just divorced.
For the second possibility, there are canonical (not OC) four candidates to be Phineas and Candace’s father.
1. Dr. Heinz Doofenshmirtz
This candidate is most well-known to the fans of P & F, the evil scientist who wants to rule the Tri-State Area. The source mostly came from here and here. Below are the supporting and opposing factors, and the stretch of it.
Many fans have believed that because they’re face structure is the same (being triangle), having hair sprouts, and have the same hobbies, Dr. Doofenshmirtz is Phineas’ biological father.
Turn to Oppose
If you look closely, their facial features are different. Heinz Doofenshmirtz has a long pointy nose and a long chin, while Phineas looks mostly like a fish.
In the episode “What Do It Do?”, Doofenshmirtz had claimed that he met Linda Flynn before, being on a date and stuff, but after he tries to use his invention, the date didn’t went well and he never met her again.
Turn to Support
If we try to stretch this up, it would go to a mature, 18+ measure. Dr. D would meet Linda and made her pregnant without noticing that she is Linda. She may be on drugs or something (thinks of Forest Gump). This may be the reason that he had been divorced to his previous wife. However, some event like this would usually occur to either one of the children.
2. Roger Doofenshmirtz
Ah, Roger. Heinz’s little brother who does many things better than him (except for inventng stuff). He doesn’t make much of an appearance, so I’m only going to put factors only.
He is Heinz’s brother. Therefore he could bring his genes to his children Candace and Phineas.
See Heinz’s Turn to oppose factors above.
3. Perry the Platypus
Yeah, you must have been wonder why an animal be a human’s biological father. You see, one of the posts on this blog explains the story of this candidate. For short, it says that Perry used to be a human who was later changed into a platypus.
Perry cares so much for the Flynn-Fletcher family. He is also mature compared to the other agents he works with. Then, in “Phineas and Ferb Get Busted”, Perry dreams of Candace dreaming something. There’s a “Little Brothers” song sequence, where every moment since Phineas was born. Also, this the ending turned out to be Perry’s dream, he seems to know a lot.
Turn to Oppose
Perry may care about the Flynn-Fletcher family because they have token care of Perry very much. In the “Little Brothers” sequence, Perry might be randomly guessing what would Phineas and Ferb’s past would be like.
Perry’s organization, the O.W.C.A, wouldn’t accept non-animal agents (except for Planty the Potted Plant). There is also so far no special relationship between Perry and Linda Flynn, his supposed “wife”.
Turn to Support
The O.W.C.A. may only had Perry the human as an agent. After he was turned into a platypus, they trained some animals to be an agent. Perry wouldn’t really want to relate himself to Linda because he is probably jealous or that’s part of acting as a normal pet platypus. He would probably care more of his “children”.
A Wild Mass Guessing from TV Tropes had stated that Norm is Mr. Flynn. The troper (term for a TV Tropes user) said that he was a human found by Dr. Doofenshmirtz turned into a robot. There’s not much proof if this is mostly possible or impossible.
After you have read the information above, it is actually up to you which one is the father, since I doubt that the creators of Phineas and Ferb would explicitly show any information about that.